51 lines
1.3 KiB
Plaintext
51 lines
1.3 KiB
Plaintext
# Solvated 5-mer peptide
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#----------------------------------
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# Taken as is from examples/peptide
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units real
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atom_style full
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boundary p p p
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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#----------------------------------
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# temperature schedule for REMD
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variable idx world 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
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variable t world 200.0 209.0 219.0 230.0 241.0 252.0 264.0 276.0 289.0 303.0 317.0 332.0 348.0 365.0 382.0 400.0
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# thermostat
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fix thermostat all langevin $t $t 1000 772530
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# log-file output before minimization
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thermo_style custom step temp ke pe
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thermo 20
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# minimization
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minimize 1e-4 0.0 1000 1000
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# change logfile output after minimization
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thermo_style custom step temp pe
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thermo 20
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# trajectory style
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dump myDump all atom 20 peptide.${idx}.lammpstrj.gz
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dump_modify myDump sort id scale no
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# run REMD (for realistic results run for 100000000 steps with 10000 frequency)
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reset_timestep 0
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temper 2000 10 $t thermostat 3847 5382
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